PRMT3

protein arginine methyltransferase 3, the group of 7BS protein arginine methyltranferases

Basic information

Region (hg38): 11:20387558-20509338

Previous symbols: [ "HRMT1L3" ]

Links

ENSG00000185238 ∙ NCBI:10196 ∙ OMIM:603190 ∙ HGNC:30163 ∙ Uniprot:O60678 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRMT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRMT3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			34		1	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	0	1

Variants in PRMT3

This is a list of pathogenic ClinVar variants found in the PRMT3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-20388025-G-A		not specified	Uncertain significance (Jul 22, 2024)
11-20388028-G-A		not specified	Uncertain significance (Feb 16, 2023)
11-20388071-C-A		not specified	Uncertain significance (Dec 05, 2022)
11-20392925-T-C		not specified	Uncertain significance (Dec 17, 2023)
11-20395810-A-T		not specified	Uncertain significance (May 10, 2024)
11-20395824-C-T		not specified	Uncertain significance (Jul 05, 2024)
11-20395851-A-G		not specified	Uncertain significance (Jun 17, 2024)
11-20395869-C-T		not specified	Uncertain significance (Sep 08, 2024)
11-20395895-A-G		not specified	Uncertain significance (Nov 17, 2023)
11-20395940-C-T		not specified	Uncertain significance (Apr 11, 2023)
11-20395941-G-A		not specified	Uncertain significance (May 15, 2023)
11-20397605-A-C		not specified	Uncertain significance (Oct 26, 2021)
11-20397605-A-G		not specified	Likely benign (Feb 22, 2025)
11-20397645-C-T			Benign (Jun 29, 2018)
11-20397701-A-T		not specified	Uncertain significance (Dec 21, 2021)
11-20397705-A-G		not specified	Uncertain significance (Dec 23, 2024)
11-20402944-G-A		not specified	Uncertain significance (Feb 10, 2022)
11-20402968-A-G		not specified	Uncertain significance (Apr 07, 2023)
11-20402973-T-C		not specified	Uncertain significance (Aug 13, 2021)
11-20407921-A-T		not specified	Uncertain significance (Sep 29, 2023)
11-20407932-G-A		not specified	Uncertain significance (Sep 10, 2024)
11-20407990-T-C		not specified	Uncertain significance (Jan 20, 2025)
11-20426773-A-G		not specified	Uncertain significance (Aug 10, 2021)
11-20452131-G-A		not specified	Uncertain significance (Dec 18, 2023)
11-20452156-G-A		not specified	Uncertain significance (Jun 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRMT3	protein_coding	protein_coding	ENST00000331079	16	121765

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.90e-25	0.0000864	125678	0	70	125748	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0999	279	284	0.983	0.0000140	3507
Missense in Polyphen		54	75.71	0.71325		993
Synonymous	0.879	91	102	0.889	0.00000540	956
Loss of Function	-0.625	35	31.2	1.12	0.00000151	400

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000911	0.000892
Ashkenazi Jewish	0.000205	0.000198
East Asian	0.000496	0.000489
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000301	0.000299
Middle Eastern	0.000496	0.000489
South Asian	0.000202	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Methylates (mono and asymmetric dimethylation) the guanidino nitrogens of arginyl residues in some proteins.
• Pathway: Histidine Metabolism;Histidinemia;Post-translational protein modification;Metabolism of proteins;RMTs methylate histone arginines;Chromatin modifying enzymes;Chromatin organization;Protein methylation (Consensus)

Recessive Scores

• pRec: 0.159

Intolerance Scores

• rvis_EVS: -0.38
• rvis_percentile_EVS: 28.01

Haploinsufficiency Scores

• pHI: 0.232
• hipred: Y
• hipred_score: 0.564
• ghis: 0.631

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Prmt3
• Phenotype: embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; immune system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: regulation of transcription, DNA-templated;protein methylation;peptidyl-arginine methylation, to asymmetrical-dimethyl arginine;negative regulation of protein ubiquitination;histone arginine methylation
• Cellular component: nucleus;cytoplasm;cytosol
• Molecular function: nucleic acid binding;protein binding;methyltransferase activity;histone-arginine N-methyltransferase activity;protein-arginine N-methyltransferase activity;protein-arginine omega-N asymmetric methyltransferase activity;ribosome binding;metal ion binding